Structure of PDB 3qgd Chain B Binding Site BS01

Receptor Information
>3qgd Chain B (length=515) Species: 31647 (Hepatitis C virus subtype 1b) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMSYTWTGALITPCSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKAST
VKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLL
EDTETPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYD
VVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDST
VTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYR
RCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESA
GTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDAS
GKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMT
HFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSY
SPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFN
WAVRTKLKLTPIPAA
Ligand information
Ligand ID23E
InChIInChI=1S/C38H38N4O5/c43-32-23-42-31-22-26(15-18-29(31)34(25-8-2-1-3-9-25)35(42)28-10-4-5-11-30(28)40-32)36(46)41-38(20-6-7-21-38)37(47)39-27-16-12-24(13-17-27)14-19-33(44)45/h4-5,10-19,22,25H,1-3,6-9,20-21,23H2,(H,39,47)(H,40,43)(H,41,46)(H,44,45)/b19-14+
InChIKeyHDBNVTWMHMMKNY-XMHGGMMESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1ccc2c(c1)-c3c(c4ccc(cc4n3CC(=O)N2)C(=O)NC5(CCCC5)C(=O)Nc6ccc(cc6)/C=C/C(=O)O)C7CCCCC7
CACTVS 3.370OC(=O)/C=C/c1ccc(NC(=O)C2(CCCC2)NC(=O)c3ccc4c(c3)n5CC(=O)Nc6ccccc6c5c4C7CCCCC7)cc1
ACDLabs 12.01O=C(O)\C=C\c1ccc(cc1)NC(=O)C7(NC(=O)c4ccc3c(c2c5c(NC(=O)Cn2c3c4)cccc5)C6CCCCC6)CCCC7
OpenEye OEToolkits 1.7.0c1ccc2c(c1)-c3c(c4ccc(cc4n3CC(=O)N2)C(=O)NC5(CCCC5)C(=O)Nc6ccc(cc6)C=CC(=O)O)C7CCCCC7
CACTVS 3.370OC(=O)C=Cc1ccc(NC(=O)C2(CCCC2)NC(=O)c3ccc4c(c3)n5CC(=O)Nc6ccccc6c5c4C7CCCCC7)cc1
FormulaC38 H38 N4 O5
Name(2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid
ChEMBLCHEMBL1738707
DrugBank
ZINCZINC000059826499
PDB chain3qgd Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3qgd Investigation of the mode of binding of a novel series of N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamides to the hepatitis C virus polymerase.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		L392 A395 A396 I424 H428 L492 G493 V494 P495 P496 R498 V499 W500 R503
Binding residue
(residue number reindexed from 1)		L365 A368 A369 I397 H401 L465 G466 V467 P468 P469 R471 V472 W473 R476
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.48: RNA-directed RNA polymerase.
3.4.21.98: hepacivirin.
3.4.22.-
3.6.1.15: nucleoside-triphosphate phosphatase.
3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003968 RNA-dependent RNA polymerase activity
Biological Process
GO:0039694 viral RNA genome replication

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:3qgd, PDBe:3qgd, PDBj:3qgd
PDBsum3qgd
PubMed21441029
UniProtQ9WMX2|POLG_HCVCO Genome polyprotein

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